why include an instance that doesn’t?
Because it lets you see how common or uncommon defederations are relative to the total set of all instances (or at least, all minus the long tail of very-low-user-count ones). And although it would make the graph larger, it would also make it sparse and IMO that would also be easier to read.
It could also give a misleading impression that all instances defederate or are defederated by somebody, making people think it's more common than it actually is. (Or maybe not doing that, if you include allish instances and it still ends up being not very sparse.)
Meanwhile, I recently got new prescription glasses (after wearing my previous pairs for way too long, BTW) and got some that have an IR-blocking coating that's supposed to block face recognition cameras. Because that apparently needs to be a thing these days.
(I'm disappointed that these DuckDuckGo glasses don't have a similar special coating. I like the company I got mine from, but I'd like to see more companies offering privacy-enhancing tech.)